scholarly journals In Situ Assessment of Intrinsic Strength of X-I⋯OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1589 ◽  
Author(s):  
Yunwen Tao ◽  
Yue Qiu ◽  
Wenli Zou ◽  
Sadisha Nanayakkara ◽  
Seth Yannacone ◽  
...  
Keyword(s):  
Bond Strength ◽  
Vibrational Mode ◽  
Halogen Bond ◽  
Molecular Crystals ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
Mode Theory ◽  
Local Vibrational Mode ◽  
Intrinsic Strength

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ -hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n → σ ∗ (X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.

scholarly journals Halogen Bonding in the Complexes of Brominated Electrophiles with Chloride Anions: From a Weak Supramolecular Interaction to a Covalent Br–Cl Bond

Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1075
Author(s):  
Cody Loy ◽  
Matthias Zeller ◽  
Sergiy V. Rosokha
Keyword(s):  
Bond Strength ◽  
Halogen Bond ◽  
Covalent Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
Nucleophilic Reaction ◽  
X Ray ◽  
Wide Range ◽  
Judicious Choice ◽  
Range Variation

The wide-range variation of the strength of halogen bonds (XB) not only facilitates a variety of applications of this interaction, but it also allows examining the relation (and interconversion) between supramolecular and covalent bonding. Herein, the Br…Cl halogen bonding in a series of complexes of bromosubstituted electrophiles (R-Br) with chloride anions were examined via X-ray crystallographic and computational methods. Six co-crystals showing such bonding were prepared by evaporation of solutions of R-Br and tetra-n-propylammonium chloride or using Cl− anions released in the nucleophilic reaction of 1,4-diazabicyclo[2.2.2]octane with dichloromethane in the presence of R-Br. The co-crystal comprised networks formed by 3:3 or 2:2 halogen bonding between R-Br and Cl−, with the XB lengths varying from 3.0 Å to 3.25 Å. Analysis of the crystallographic database revealed examples of associations with substantially longer and shorter Br…Cl separations. DFT computations of an extended series of R–Br…Cl− complexes confirmed that the judicious choice of brominated electrophile allows varying halogen Br…Cl bond strength and length gradually from the values common for the weak intermolecular complexes to that approaching a fully developed covalent bond. This continuity of halogen bond strength in the experimental (solid-state) and calculated associations indicates a fundamental link between the covalent and supramolecular bonding.

scholarly journals Thermomechanical effect in molecular crystals: the role of halogen-bonding interactions

IUCrJ ◽  
2017 ◽  
Vol 4 (6) ◽  
pp. 812-823 ◽  
Author(s):  
Sudhir Mittapalli ◽  
D. Sravanakumar Perumalla ◽  
Jagadeesh Babu Nanubolu ◽  
Ashwini Nangia
Keyword(s):  
Bond Strength ◽  
Thermal Effects ◽  
Halogen Bond ◽  
Molecular Crystals ◽  
Thermal Response ◽  
Halogen Bonding ◽  
Cell Parameters ◽  
Design And Synthesis ◽  
Compound C ◽  
Thermomechanical Effect

The design and synthesis of mechanically responsive materials is interesting because they are potential candidates to convert thermal energy into mechanical work. Reported in this paper are thermosalient effects in a series of halogen derivatives of salinazids. The chloro derivative, with higher electronegativity and a weaker inter-halogen bond strength (Cl...Cl) exhibits an excellent thermal response, whereas the response is weaker in the iodo derivative with stronger I...I halogen bonding. 3,5-Dichlorosalinazid (Compound-A) exists in three polymorphic forms, two room-temperature polymorphs (Forms I and II) and one high-temperature modification (Form III). The transformation of Form I to Form III upon heating at 328–333 K is a reversible thermosalient transition, whereas the transformation of Form II to Form III is irreversible and non-thermosalient. 3,5-Dibromo- (Compound-B) and 3-bromo-5-chloro- (Compound-C) salinazid are both dimorphic: the Form I to Form II transition in Compound-B is irreversible, whereas Compound-C shows a reversible thermosalient effect (362–365 K). In the case of 3,5-diiodosalinazid (Compound-D) and 3,5-difluorosalinazid (Compound-E), no phase transitions or thermal effects were observed. The thermosalient behaviour of these halosalinazid molecular crystals is understood from the anisotropy in the cell parameters (an increase in theaaxis and a decrease in thebandcaxes upon heating) and the sudden release of accumulated strain during the phase transition. The di-halogen salinazid derivatives (chlorine to iodine) show a decrease in thermal effects with an increase in halogen-bond strength. Interestingly, Compound-B shows solid-state photochromism in its polymorphs along with the thermosalient effect, wherein Form I is cyan and Form II is light orange.

scholarly journals Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons

2020 ◽  
Vol 21 (18) ◽  
pp. 6571
Author(s):  
Nicholas J. Thornton ◽  
Tanja van Mourik
Keyword(s):  
Base Pair ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Dna Bases ◽  
Halogen Bonds ◽  
Base Pairs ◽  
Rich Diversity ◽  
Different Types ◽  
Guanine Base ◽  
The Stability

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).

scholarly journals Characterizing the interplay of Pauli repulsion, electrostatics, dispersion and charge transfer in halogen bonding with energy decomposition analysis

2018 ◽  
Vol 20 (2) ◽  
pp. 905-915 ◽  
Author(s):  
Jonathan Thirman ◽  
Elric Engelage ◽  
Stefan M. Huber ◽  
Martin Head-Gordon
Keyword(s):  
Charge Transfer ◽  
Bond Strength ◽  
Halogen Bond ◽  
Decomposition Analysis ◽  
Halogen Bonding ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Pauli Repulsion

Variational energy decomposition analysis establishes charge-transfer as the origin of halogen bond strength differences that go against electrostatics.

scholarly journals Study of the Halogen Bonding between Pyridine and Perfluoroalkyl Iodide in Solution Phase Using the Combination of FTIR and 19F NMR

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Briauna Hawthorne ◽  
Haiyan Fan-Hagenstein ◽  
Elizabeth Wood ◽  
Jessica Smith ◽  
Timothy Hanks
Keyword(s):  
Halogen Bond ◽  
Equilibrium Constants ◽  
Binding Constants ◽  
Halogen Bonding ◽  
Blue Shift ◽  
Halogen Bonds ◽  
Perfluoroalkyl Iodide ◽  
Solvent Dependence ◽  
Dilution Experiments ◽  
Stretching Vibrations

Halogen bonding between pyridine and heptafluoro-2-iodopropane (iso-C3F7I)/heptafluoro-1-iodopropane (1-C3F7I) was studied using a combination of FTIR and 19F NMR. The ring breathing vibration of pyridine underwent a blue shift upon the formation of halogen bonds with both iso-C3F7I and 1-C3F7I. The magnitudes of the shifts and the equilibrium constants for the halogen-bonded complex formation were found to depend not only on the structure of the halocarbon, but also on the solvent. The halogen bond also affected the Cα-F (C-F bond on the center carbon) bending and stretching vibrations in iso-C3F7I. These spectroscopic effects show some solvent dependence, but more importantly, they suggest the possibility of intermolecular halogen bonding among iso-C3F7I molecules. The systems were also examined by 19F NMR in various solvents (cyclohexane, hexane, chloroform, acetone, and acetonitrile). NMR dilution experiments support the existence of the intermolecular self-halogen bonding in both iso-C3F7I and 1-C3F7I. The binding constants for the pyridine/perfluoroalkyl iodide halogen bonding complexes formed in various solvents were obtained through NMR titration experiments. Quantum chemical calculations were used to support the FTIR and 19F NMR observations.

scholarly journals Hydrogen and Halogen Bond Mediated Coordination Polymers of Chloro-Substituted Pyrazin-2-Amine Copper(I) Bromide Complexes

Chemistry ◽  
2020 ◽  
Vol 2 (3) ◽  
pp. 700-713
Author(s):  
Aaron Mailman ◽  
Rakesh Puttreddy ◽  
Manu Lahtinen ◽  
Noora Svahn ◽  
Kari Rissanen
Keyword(s):  
Coordination Polymers ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
X Ray Diffraction ◽  
New Class ◽  
Monodentate Ligands ◽  
High Yields ◽  
Polymeric Structures ◽  
Mode Of Coordination

A new class of six mono- (1; 3-Cl-, 2; 5-Cl-, 3; 6-Cl-) and di-(4; 3,6-Cl, 5; 5,6-Cl-, 6; 3,5-Cl-) chloro-substituted pyrazin-2-amine ligands (1–6) form complexes with copper (I) bromide, to give 1D and 2D coordination polymers through a combination of halogen and hydrogen bonding that were characterized by X-ray diffraction analysis. These Cu(I) complexes were prepared indirectly from the ligands and CuBr2 via an in situ redox process in moderate to high yields. Four of the pyrazine ligands, 1, 4–6 were found to favor a monodentate mode of coordination to one CuI ion. The absence of a C6-chloro substituent in ligands 1, 2 and 6 supported N1–Cu coordination over the alternative N4–Cu coordination mode evidenced for ligands 4 and 5. These monodentate systems afforded predominantly hydrogen bond (HB) networks containing a catenated (μ3-bromo)-CuI ‘staircase’ motif, with a network of ‘cooperative’ halogen bonds (XB), leading to infinite polymeric structures. Alternatively, ligands 2 and 3 preferred a μ2-N,N’ bridging mode leading to three different polymeric structures. These adopt the (μ3-bromo)-CuI ‘staircase’ motif observed in the monodentate ligands, a unique single (μ2-bromo)-CuI chain, or a discrete Cu2Br2 rhomboid (μ2-bromo)-CuI dimer. Two main HB patterns afforded by self-complimentary dimerization of the amino pyrazines described by the graph set notation R22(8) and non-cyclic intermolecular N–H∙∙∙N’ or N–H∙∙∙Br–Cu leading to infinite polymeric structures are discussed. The cooperative halogen bonding between C–Cl∙∙∙Cl–C and the C–Cl∙∙∙Br–Cu XB contacts are less than the sum of the van der Waals radii of participating atoms, with the latter ranging from 3.4178(14) to 3.582(15) Å. In all cases, the mode of coordination and pyrazine ring substituents affect the pattern of HBs and XBs in these supramolecular structures.

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